Using synthetic signaling to reprogram plants.

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Abstract

To engineer plants that can address the environmental challenges posed to agriculture we need to be able to rationally design their developmental and stress response phenotypes. To achieve this larger goal, we first need to understand the native mechanisms that control these processes. More specifically, we need to understand the mechanisms behind the flow of information, i.e. some change of state that can propagate through a biological system like a signal through a circuit, in biological systems, as this process is the driver for most multicellular development and stress response phenotypes. Information flow occurs at every level in biological systems, whether from one sub-domain of a protein to another, or from a caterpillar to the plant it is eating. The form this information takes also varies, including phosphorylation events and the production of small molecule hormones. A great deal of work has been done to understand the fundamental molecular mechanisms driving these signal transduction systems and how coordinated signaling events can lead to cell and organism level phenotypes. This understanding can be leveraged to design novel synthetic systems to either alter or replace these mechanisms to achieve the phenotypes of interest. The field of synthetic biology has made great strides in both developing strategies to reengineer native signaling machinery as well as designing totally synthetic signaling systems. This work has, until recently, been limited to microbes due to their fast generation times which makes prototyping new synthetic signaling systems a more rapid process than is possible in multicellular eukaryotes like plants and animals. However, it has provided a great deal of transferable knowledge and parts, which have made translating these systems into larger organisms a less daunting prospect. There are still major challenges to applying synthetic biology in higher eukaryotes such as relatively more difficult transformation process and heterogeneity across tissues, but we are now poised to leverage these powerful tools for biological engineering. Here I describe how I used synthetic signaling systems at a range of scales to both learn more about native plant signaling as well as to develop programmable phenotypes in plants. The first few chapters cover work to prototype synthetic signaling systems in vitro and in the more tractable model organism, Saccharomyces cerevisiae. The later chapters describe how we used some of these tools to learn more about the natural signaling systems in the model plant, Arabidopsis thaliana, and to re-program its development and stress response phenotypes.